Noah K. Murray/The Star-LedgerHome Plate umpire Jerry Layne calls Mets shortstop Jose Reyes out at third after Reyes attempted a stolen base in the seventh inning of the Subway Series opener against the Yankees at Citi Field tonight.

NEW YORK — In the flash point of the first game of the second leg of the Subway Series, his eyes told the story. After Mets shortstop Jose Reyes slid into third base, apparently beneath the tag of Yankees third baseman Alex Rodriguez, he stared upward at the umpire, awaiting a safe call that never came.

Jerry Layne’s pumped fist in the seventh inning set off a chain reaction: Reyes raged as he left the diamond. Manager Terry Collins got himself thrown out. The Mets, trailing by two runs at the time, had their best chance to even the score disappear, and the Yankees left Citi Field with a 5-1 victory tonight in front of 42,020 fans, the largest crowd in the history of this ballpark.

The Yankees (49-31), who have won six in a row, benefited from a three-run first inning off Jon Niese. They remained in front due to a decent performance from Ivan Nova, sending the Mets (41-41) back to .500.

Niese lasted six innings. At the outset, he felt compelled to avoid his off-speed options. In the first three innings, he threw 50 pitches. Eight were curveballs. The rest were a stew of four-seamers, two-seamers and cutters. The Yankees benefited from the monotony.

In the first inning, the Yankees ambushed him. Nick Swisher cracked a fastball for a single. Curtis Granderson lined a single to right. Both scored four pitches later when Mark Teixeira, after missing a curveball, sliced a double into the right-field corner.

From the dugout bounded manager Collins. Last weekend in Texas, Niese labored with a rapid heartbeat, a condition known as tachycardia he has dealt with often on the mound. The issue here did not appear physical. Collins spoke with Niese for a few moments, then jogged off the field.

The pow-wow was not immediately beneficial. After Rodriguez grounded out, a line drive by Robinson Cano flew over the head of left fielder Jason Bay for a run-scoring double.

In the second, the Mets notched a run off Nova, who spread seven hits over his five innings. First, Bay poked a 1-2 curve into right for an opposite-field single. He bounded to third on a single by Ronny Paulino.

With one out, Ruben Tejada came to the plate. He did not remain there long. Nova missed low with a fastball, then threw a 94-mph heater down the middle. Tejada dumped it into center to score Bay. The rally soon fizzled, when Nova struck out Niese and forced Reyes to bounce into a groundout.

By then, Niese had begun to mix up his arsenal. He froze Granderson with a curveball to end the second. He repeated that pattern with Swisher in the fourth. Granderson whiffed on another curve to open the fifth.

Yet the Yankees retained their advantage. Nova settled into a groove. After he gave up three hits in the second, he began piling up ground-ball outs. Five of his next six outs were accrued on the ground.

The Mets had a chance to do some damage against Nova in the fifth. Justin Turner tagged a two-out single to left. Carlos Beltran ripped a single to right. Daniel Murphy worked a walk to load the bases.

Pitching coach Larry Rothschild entered the fray. He steadied Nova as Angel Pagan came to the plate. The pace became agonizing. Down 1-2, Pagan grazed a curveball to keep the at-bat alive. He stared at another curveball, this one outside. Then Nova pumped another breaking ball, barreling toward the dirt. Pagan swung through it.

On the other end, Niese’s curve kept him alive. With the bases loaded, Yankees manager Joe Girardi pulled Nova so Jorge Posada could hit. Niese spun a curveball past him for strike three. Swisher grounded out to keep the score 3-1.